There are plastic L shaped pieces that cover those holes and they have the holes in them for the bed tie downs. supposed to suck it up to the front and sides.
They have longer bolts for the tie downs to accommodate the extra thickness as well.
I would not use a drop in liner. My experience shows that dirt collects under the liners and with road vibration will abrade the paint down to the metal. Soon you will have hidden rust. With the small amount of steel coated with galvanize you will soon have the steel rust out between the very thin layers of galvanize leaving you with two layers of "tin foil" for body panels. I had a 2001 7.3 and after removing the drop in liner shortly thereafter I was in the bed and my foot fell through the floor. A very small amount of visible rust proved to be a disaster since the rust extended between the layers of galvanize. If you spot rust you need to immediately treat and stop any further corrosion or you will have a fate like mine.
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